Re: [PyMOL] Fuse gaps

Hi Alex,

the gaps and the scrambled sequence view have the same reason, it's the
internal ordering of atoms which is not consecutive. PyMOL does this
based on atom identifiers (chain, resi, etc.). I suggest assigning
ascending chain letters to the three parts before fusing.

alter nterminus, chain='A'
alter middlesub, chain='B'
alter cterminus, chain='C'
fuse ...

Cheers,
  Thomas

Alex Truong wrote, On 11/26/12 22:31:
> Hi All,
> 
> I recall asking a bunch of questions here about Fuse earlier this year,
> but I haven't needed to come back to it until now. Apologies if this has
> already been addressed elsewhere.
> 
> When I fuse, the two objects are manually attached in a reasonable way,
> correct? Does the cartoon representation accurately reflect that
> attachment? I just fused 3 subunits together, and there are some fairly
> noticeable gaps between subunits when looking at the cartoon view. Even
> though they look properly fused from the line view, since our
> publication will rely on the cartoon view for simplicity, these gaps
> are...unacceptable. Does anyone know the reason for them, and how to fix
> them? Additionally, the residue order in the sequence view is scrambled.
> They are attached in the correct order, but the middle subunit is
> displayed first, then the N-terminus, then the C-terminus.
> 
> Thanks,
> 
> Alex Truong

-- 
Thomas Holder
PyMOL Developer
Schrödinger Contractor